How can I gene names from gene IDs (Arabidopsis)?

Question

[huang2]

Hi all,

I have a list of DE genes (gene ID) from my RNAseq data. This list contains around one thousand genes. How can I get these gene's names?

Thanks

Jian

[Neilfws]

We need to see some examples of IDs and names. But the answer is likely to be: use BioMart.

[Emily]

Not sure how to use it, here's Giulietta telling you how.

[huang2]

Thanks Daniel. Sorry I did not follow up my own question since I had some health troubles and was not available to reply you. Now I solved this problem based on your advice. Thanks a lot.

Jian

[Daniel]

Glad to help! Click the "accept answer" tick button to say it's answered if it's the case!

Answer 1

[Daniel]

You should look at Thalemine from Araport. They have the latest Arabidopsis annotations (most other sites are still using the TAIR10 which is a bit outdated now (Reference)).

Here's their search page.

Alternatively, you can do it via the API which they give templates for. Here is one I bodged from their script for pulling ontologies in bulk rather than one at a time:

$ thalemine_query genelist.txt

#!/usr/bin/env python

import sys

# This is an automatically generated script to run your query
# to use it you will require the intermine python client.
# To install the client, run the following command from a terminal:
#
#     sudo easy_install intermine
#
# For further documentation you can visit:
#     http://intermine.readthedocs.org/en/latest/web-services/

# The following two lines will be needed in every python script:
from intermine.webservice import Service
service = Service("https://apps.araport.org:443/thalemine/service")

# Read file with list of genes for searching.
gene_list_file = sys.argv[1]
gene_list = open(gene_list_file, "rU")

# Get a new query on the class (table) you will be querying:
for gene in gene_list:
    gene = '"' + gene.rstrip() + '"'
    print gene
    query = service.new_query("Gene")

# The view specifies the output columns
    query.add_view(
        "primaryIdentifier", "symbol", "name", "pathways.identifier",
        "pathways.name"
    )

# Uncomment and edit the line below (the default) to select a custom sort order:
# query.add_sort_order("Gene.primaryIdentifier", "ASC")

# You can edit the constraint values below

    query.add_constraint("Gene", "LOOKUP", gene , "A. thaliana", code = "A")

# Uncomment and edit the code below to specify your own custom logic:
# query.set_logic("A")

    for row in query.rows():
        print row["primaryIdentifier"], row["symbol"], row["name"], row["pathways.identifier"], \
            row["pathways.name"]